I would "substitute" Osaka for Yokohama and Kyoto for Kamakura. It is definitely not the same, but given the timeframe I believe they might suit you better.

My favorite Tokyo plan starts by waking up early to do people watching at the Shibuya Starbucks, then walking to Harajuku for touring Meiji Jingu, spend a little while cheking out toys at Kiddy Land and having lunch around Omote Sando.

After lunch I would move to the Shinbashi area, visiting the Hama Rikyu garden and later jumping aboard the Yurikamome line to Odaiba. There I would check out the giant Gundam, and go wait for sunset at Aqua City, with the beautiful view of the Rainbow bridge as it's lights are turned on.

Finally I would return to Shinbashi for dinner, probably yakitori and beer under the bridges, but maybe something fancier if the mood strikes.

Stay in Merida. the city itself id very nice, there are wonderful places all around (Chichen Itzá, the flamingos at Celestum, The Puuc rute, Izamal, lots of Cenotes, etc.) and Cancun is not far away (3 hours, I believe).